org.biopax.paxtools.impl

Class BioPAXElementImpl

java.lang.Object

org.biopax.paxtools.impl.BioPAXElementImpl

All Implemented Interfaces:

Serializable, Cloneable, BioPAXElement

Direct Known Subclasses:

L3ElementImpl

public abstract class BioPAXElementImpl
extends Object
implements BioPAXElement

See Also:

Serialized Form

Field Summary

Fields inherited from interface org.biopax.paxtools.model.BioPAXElement

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Constructor Summary

Constructors

Constructor and Description
BioPAXElementImpl()

Method Summary

Modifier and Type	Method and Description
boolean	equals(Object obj) true if and only if the other obj has the same biopax type (same BioPAXElement.getModelInterface(), not a subclass) and same URI.
int	equivalenceCode() If two elements are equivalent, then their equivalence code should be the same.
Map<String,Object>	getAnnotations() A general-purpose map to optionally store additional application-specific information about the BioPAX element, such as statistics, inferred fields, etc.
String	getUri() This method returns the absolute URI of the element.
int	hashCode() This method is consistent with the overridden equals(Object) method (biopax type and URI are what matters)
boolean	isEquivalent(BioPAXElement element) This method compares the given element for equivalency.
protected boolean	semanticallyEquivalent(BioPAXElement element)
String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.biopax.paxtools.model.BioPAXElement

getModelInterface

Constructor Detail

BioPAXElementImpl

public BioPAXElementImpl()

Method Detail

isEquivalent

public boolean isEquivalent(BioPAXElement element)

Description copied from interface: BioPAXElement

This method compares the given element for equivalency. This is different from equals(), as BioPAX elements resolve equality based on URI. Equivalent returns true if elements are equal or if

• both elements implement the same model interface AND
• both elements have equivalent key properties

These key properties vary from class to class.

Specified by:

isEquivalent in interface BioPAXElement

Parameters:

element - to be compared for equivalency

Returns:

true if the element equals to this, or has equivalent critical properties.

semanticallyEquivalent

protected boolean semanticallyEquivalent(BioPAXElement element)

equivalenceCode

public int equivalenceCode()

Description copied from interface: BioPAXElement

If two elements are equivalent, then their equivalence code should be the same.

Specified by:

equivalenceCode in interface BioPAXElement

Returns:

an integer that is same across all equivalent entities.

getUri

public String getUri()

Description copied from interface: BioPAXElement

This method returns the absolute URI of the element. BioPAX data providers are responsible for generating globally unique and standard URIs for their BioPAX elements.

Specified by:

getUri in interface BioPAXElement

Returns:

unique URI for this object.

toString

public String toString()

Overrides:

toString in class Object

getAnnotations

public Map<String,Object> getAnnotations()

Description copied from interface: BioPAXElement

A general-purpose map to optionally store additional application-specific information about the BioPAX element, such as statistics, inferred fields, etc.

Specified by:

getAnnotations in interface BioPAXElement

Returns:

additional (not BioPAX standard) annotations

equals

public boolean equals(Object obj)

true if and only if the other obj has the same biopax type (same BioPAXElement.getModelInterface(), not a subclass) and same URI. Other properties are not considered.

Overrides:

equals in class Object

hashCode

public int hashCode()

This method is consistent with the overridden equals(Object) method (biopax type and URI are what matters)

Overrides:

hashCode in class Object